Debraj Ghose

How can cells self-organize rapidly into complex patterns during development?

Let’s explore a powerful and underappreciated mechanism: Directed Cell Migration (DCM).

Preprint @biorxivpreprint.bsky.social : doi.org/10.1101/2025...

👇Thread 🧵(1/11)

Beautiful!!

Such an honor to be featured by @focalplane.bsky.social , especially on my favorite day of the week: #FluorescenceFriday! 🔬

Below for reference, a picture of the full hydei testis with the musculature stained (depth-coded) taken together with @saraheclark.bsky.social

#cellbio #devbio #microscopy

Happy #FluorescenceFriday !!! Pt 2: fungal hyphae challenged with various oxidative stressors; nucleic acids - yellow, ROS - magenta feat. bubbles induced by H2O2 from earlier imaging experiments when I had no idea what I was doing :)

Stimulating immune cells in vitro is a common experimental lab model. We profiled 150K blood immune cells treated with 11 different stimuli to compare the effects. The data are freely available for researchers. See the preprint for our findings and to access the data 🧪 doi.org/10.1101/2025...

FINALLY out in #Science Advances! 🎉
3 years of hard work, a fantastic team — and I’m proud to be first and co-corresponding author!

It's about Plexin signaling driving collective cell migration & organ sculpting. Check out the videos 😀

www.science.org/doi/10.1126/...

#DevBio #CellBio #Microscopy

3D printed microscopy we could perhaps try in the lab

onlinelibrary.wiley.com/doi/10.1111/...

#GLSL #Shaders

HIGH-RESOLUTION IN VIVO BRAIN IMAGING OF DROSOPHILA 🪰
New Preprint by Tassara et al.!

www.biorxiv.org/content/10.1...
#FluorescenceMonday #SnoutClub 1/6

A perfectly round liver organoid stained for mitochondria (yellowish/green), e-cadherin in blue and nuclei in pink for #MicroscopyMonday

Pretty!

Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images Author summary Bacteria organize themselves on surfaces in ways that influence the spread of infections, but studying these behaviors is difficult, especially when multiple species are involved or the...

Excited to share our latest paper in PLOS Comp Bio, describing how accurate, multi-species segmentation models for bacteria can be created quickly and easily using image-to-image translation. 🧪⚛️
#biophysics #imageanalysis #microscopy #AI

dx.doi.org/10.1371/jour...

Bonus: ran a quick color variation test — because it's always worth playing with presentation.
Color isn’t just style — it shapes what you see.

#MicroscopyCommunity #ScientificVisualization #Biophysics

#Microtubule-driven cell shape changes and #actomyosin flow synergize to position the #centrosome, say Alexandre Schaeffer, Manuel Théry (@manuelthery.bsky.social ) and colleagues: rupress.org/jcb/article/...

@lblanchoin.bsky.social
@gelinmatthieu.bsky.social

#Biophysics #Cytoskeleton

My #FlyWeek contribution:

The Variety of Testis Shapes in Pomace Fly Species

Aren't they beatiful?🌈🪰🔬

An old-school sci-poster meets modern confocal imaging!
#Drosophila testis diversity fascinated even Curt Stern (yes, the human genetics textbook guy!) back in the 1930s.
#microscopy #insects

indeed, i begin my grad lecture on RNAi/miRNAs by discussing petunias. and mentioning while none of our students will do a plant phd (no faculty), they can learn A LOT by occasionally reading plant literature (think epigenetics, small RNAs, developmental biology, etc etc). also, consider the worm!

What governs where DNA replication begins in human cells? Here, we show that origins of replication in human DNA are epigenetically specified and that crucially, this epigenetic mark is required for both DNA replication and cell proliferation! @narjournal.bsky.social academic.oup.com/nar/article/...

Investigating Local Negative Feedback of Rac Activity by Mathematical Models and Cell Motility Simulations For polarization and directed migration, cells use a combination of local positive feedback and long-range inhibition. We have previously used mathematical models to show the ability of this core…

If you're curious about how cells make decisions in complex environments, and how mathematical models can capture such behaviour, our preprint is now live!
Check it out here: www.biorxiv.org/content/10.1...

YouTube video by Debraj Shubham Ghose Local collective memory from ratiometric signaling outperforms cellular gradient sensing limits

Manuscript: www.biorxiv.org/content/10.1... Feedback welcome!

Talk: www.youtube.com/watch?v=A7XH...

Had a ton of fun working on this with James Nolen and Daniel Lew! Super glad Kathy Guan and Timothy Elston joined us on our adventure!

Grateful to NIH and Sloan Foundation for their support!

n/n

This strategy could underly fertilization, immune responses, embryo patterning—or allow us to build gradient-sensing microrobots for targeted drug delivery. 8/n

Schematic showing that gradient estimates by ratiometric sensing outperform estimates by classical sensing.

This local memory allows cells to average receptor signals and outperform instantaneous cellular gradient sensing limits.
— Left: classical sensing drifts.
— Right: ratiometric model stays locked on target. 7/n

We find that the ratiometric readout, which is enabled by a population of diffusing G‑proteins, generates a rolling local collective memory of past receptor states. 6/n

YouTube video by Debraj Shubham Ghose Ratiometric NG 2500 NR 375 Dm 002 Pher 8 4 1

Surprisingly, our simulations show that the ratiometric sensing strategy can outperform instantaneous physical limits of gradient detection. How??? 5/n

www.youtube.com/watch?v=B3Dg...

But cells also pay attention to the “quiet.” By comparing bound (ON) and unbound (OFF) receptors, they build a ratiometric readout. 4/n

Classic view: focus only on the “ON” beeps—molecules binding to receptors. Useful, but half the story. 3/n

Cells often infer faint signals from noisy and complex chemical landscapes—like picking out a whisper in a packed stadium. One wrong move could derail development or immunity. 2/n

YouTube video by Debraj Shubham Ghose Local collective memory from ratiometric signaling outperforms cellular gradient sensing limits

We found that cells use emergent collective memory—arising from simple chemical reactions—to outperform physical limits of detecting chemical gradients. Curious how? 1/n

8 min talk: www.youtube.com/watch?v=A7XH...

bioRxiv: www.biorxiv.org/content/10.1...

#biophysics #cellbiology

U2OS labeled with OMP25-GFP, an outer membrane marker for mitochondria.

Left shows a zoom-in on the dimmer cell.

Imaged by OPM (oblique plane microscope).

#Microscopy

Beautiful!

2x Preprint drop!!! Mitochondrial pearling has arrived!
“The Biophysical Mechanism of Mitochondrial Pearling”.
“Pearling Drives Mitochondrial DNA Nucleoid Distribution” 1/10
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...